[ccp4bb] Don't forget to register 14th Biology and Synchrotron Radiation Conference (BSR14.com) June 11 to 14 2023 in Lund, Sweden

[Marjolein Thunnissen]

We would like to remind all that the deadline for the 14th BSR conference 
registration is nearing. The meeting is being planned as a physical, on-site 
meeting, but with a virtual component to aid those who are not able to travel.
The International Biology and Synchrotron Radiation meetings are held every 
three years to present and discuss state-of-the-art applications in relevant 
research fields. They have a long-standing record since the first meeting in 
Frascati, Italy in 1986. Subsequent meetings were held at sites at or near the 
most advanced light source facilities around the world, with the last BSR 
meeting taking place in Shanghai, China in 2019. BSR is a unique forum to 
discuss the novel possibilities of synchrotrons and X-ray lasers and to promote 
their applications to challenging biological problems

The venue is in the city center of Lund (southern Sweden), only a 25 min train 
ride from Copenhagen Airport.

The conference will start with registration and a welcome reception on Sunday, 
June 11 2023. A three-day scientific program will follow, finishing in the 
afternoon of Wednesday, June 14, 2023. A limited number of subsidized student 
admissions is available.

For further information as well as a list of Keynote and Invited speakers, see 
www.BSR14.com.

We are very much looking forward to welcoming you in Lund in the Summer of 
2023. With kind regards

 For the BSR14 organizing team:

Marjolein Thunnissen, MAX IV
Filipe Maia, Uppsala University

[cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC]


Dr. Marjolein Thunnissen
Life Science Director
MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 225 94 Lund
Telephone:+46 46 2224668
Mobile:  +46 766 32 04 17
www.maxiv.lu.se









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Re: [ccp4bb] Virtual Crash Course - Understanding PDBx/mmCIF | May 3rd | REGISTER NOW!

[Gregg Crichlow]

One more reminder The course is *tomorrow*.

The RCSB Protein Data Bank will provide a course, "Use PDB data to their full 
extent: Understanding PDBx/mmCIF" on  Wednesday, May 3rd 2023 from 1:00-3:00 EDT

Understand the basics of PDBx/mmCIF data dictionary and file format that 
underpin archiving of more than 200,000 experimentally determined 
three-dimensional biostructures in the PDB. Learn about software tools for 
generating and working with PDBx/mmCIF files, and programmatic access for 
harvesting PDB data.

The program: 
https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-crash-course.pdf

Free registration: https://go.rutgers.edu/u3vpwjet

If you have questions, please contact Michelle Sanghera: 
msangh...@iqb.rutgers.edu



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Re: [ccp4bb] happy/sad maps

[Guillaume Gaullier]

Hello James,

Thank you for sharing! As usual, these messages and the answers they attract 
are very educational, and I enjoyed reading.

Regarding "all-or-nothing real space maps", in single-particle cryoEM the masks 
we use always have a soft edge (continuously and smoothly decaying from 1 to 0 
over several voxels). Some programs like Relion even let you decide how wide 
you want to make this soft edge. I don’t know enough Fourier theory to 
understand whether this is a satisfactory solution in principle, but in 
practice it seems to be good enough.

Cheers,

Guillaume


On 1 May 2023, at 01:38, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

Thanks to all who replied both on- and off-list.

A few (such as Charles below) have reported that using general-purpose FFT 
algorithms, such as those available in Matlab or NumPy do, in fact, get the 
smiley face map back.  This is expected because such algorithms do not have a 
resolution cutoff.  The programs I have found do turn the smile into a frown 
are:
phenix.fft and phenix.map_to_structure_factors in Phenix
"fft", "sfall" and "refmac5" in the CCP4 Suite

The reason why this happens is not that these programs are "buggy", but simply 
because they require the array of hkls in reciprocal space to be a sphere, not 
a cube.  That is, if h,k,l = 0,0,15 is at the resolution limit, then h,k,l = 
15,15,15 is going to be outside of it, and discarded. The smiley face consists 
entirely of these high-order structure factors.  Rejecting these "corner" 
regions may seem like a good idea until you realize that they are the only 
aspect of the map that carries happiness. ;)

But all joking aside, the reason why these programs reject the "corners" is 
because they "should" be zero.  And as long as you only ever work with maps 
that are generated from structure factors they will be zero.  If they are not 
zero, why?  And what happens if you rotate the object before recording it?  
Those non-zero "corners" will then be out beyond the faces of the cube, and 
therefore folding back into the lower-resolution data, messing it up.  This 
implies, of course, that the non-rotated object is also being messed up by 
noise beyond the Nyquist limit.  What I am suggesting is that non-zero "corner" 
regions may be a canary in our coal mine.

Paul introduced the interesting possibility of super-sampling, and what I'm 
really trying to get at here is: what is the best way to "feather" an 
all-or-nothing real-space map (such as a bulk solvent mask, or a single-pixel 
detector event), so that it does not spray noise all over reciprocal space?

Many of you may think this is a trick question and that I already have a 
beautiful answer I'm waiting to reveal.  That is not really the case.  What I 
have is a handful of rather unsatisfactory solutions, and I'm wondering if I'm 
just not aware of an existing solution to this problem.

Hope everyone had a lovely weekend,

-James Holton
MAD Scientist


On 4/28/2023 1:35 PM, Sindelar, Charles wrote:
Hi James!  I’m not sure exactly what cpp4, coot and phenix do for their FFT’s, 
but I’m assuming they must mask off the ‘corners’ of the 3D FFT data cube 
transform (where the frequency is greater than the Nyquist) during the forwards 
transform.

If you take your Cheshire map and do the FFT in matlab or octave, this is not 
done and I can confirm you get the smiley back. The cryo-EM software I am 
familiar with does filter away the FFT corners during the first 3D 
reconstruction step, so bypassing this issue.

Fun demo- this would be a great exercise for students!

Chuck


From: CCP4 bulletin board  
on behalf of James Holton 
Date: Friday, April 28, 2023 at 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK 

Subject: [ccp4bb] happy/sad maps
Its still April, but this one isn't a joke.

The smiley-face electron density in the left panel of the attached image
has the remarkable property that any attempt to sharpen or blur the map
turns it into the frowny-face on the right.  If you'd like to try this
yourself, the hidden_frown.map file is available in this tarball:
https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbl831.als.lbl.gov%2F~jamesh%2Fbugreports%2Ffft_042423.tgz=05%7C01%7Ccharles.sindelar%40YALE.EDU%7Cc059178a4b774611f6ec08db48001b68%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638182937669477928%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=jl16hGjaqmChVOHWb%2FAvgtvPTVFOt06wBqBYoxPk%2FZw%3D=0

In fact, any use of an FFT, even with the sharpening B set to zero,
turns the smiley into a frowny face. There is no way to get the smiley
face back (except opening the file again).  Yes, that's right, even just
a simple back-and-forth FFT: turning this hidden_frown.map into
structure factors and then back into a map